Copper in PDB 5obo: Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii

The structure of Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii, PDB code: 5obo was solved by J.Dong, D.Sasaki, R.Eady, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.00 / 1.89
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	180.690, 180.690, 180.690, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 17.5

The structure of Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Copper atom in the Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii (pdb code 5obo). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii, PDB code: 5obo:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu501 b:20.0 occ:1.00 ND1 A:HIS143 2.1 18.4 1.0 ND1 A:HIS94 2.1 20.3 1.0 SG A:CYS135 2.2 19.7 1.0 SD A:MET148 2.6 20.1 1.0 CE1 A:HIS143 3.0 19.7 1.0 CE1 A:HIS94 3.0 21.1 1.0 CG A:HIS143 3.1 19.2 1.0 CG A:HIS94 3.1 20.8 1.0 CB A:CYS135 3.2 18.6 1.0 CE A:MET148 3.4 19.9 1.0 CB A:HIS94 3.4 20.6 1.0 CB A:HIS143 3.5 19.7 1.0 CA A:HIS94 3.8 19.8 1.0 O A:PRO93 4.0 19.1 1.0 NE2 A:HIS143 4.1 17.3 1.0 CG A:MET148 4.1 20.2 1.0 CD2 A:HIS143 4.1 18.9 1.0 NE2 A:HIS94 4.2 20.8 1.0 CD2 A:HIS94 4.2 20.9 1.0 CB A:THR137 4.3 20.6 1.0 OG1 A:THR137 4.3 19.4 1.0 CE3 A:TRP61 4.6 19.6 1.0 N A:ASN95 4.6 18.1 1.0 CA A:HIS143 4.6 19.3 1.0 CA A:CYS135 4.6 17.7 1.0 CB A:MET148 4.6 18.6 1.0 C A:HIS94 4.8 20.0 1.0 N A:HIS94 4.8 19.9 1.0 C A:PRO93 4.8 19.9 1.0

Copper binding site 2 out of 2 in the Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitrite Bound D97N Mutant of Three-Domain Heme-Cu Nitrite Reductase From Ralstonia Pickettii within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu502 b:19.8 occ:0.70 N A:NO2506 1.8 29.7 0.7 O2 A:NO2506 1.9 24.9 0.7 NE2 A:HIS134 2.0 18.7 1.0 NE2 A:HIS99 2.0 16.5 1.0 CE1 A:HIS99 3.0 17.6 1.0 CD2 A:HIS134 3.0 17.4 1.0 CE1 A:HIS134 3.0 20.3 1.0 O1 A:NO2506 3.0 26.3 0.7 CD2 A:HIS99 3.1 16.0 1.0 ND2 A:ASN97 3.7 20.6 1.0 ND1 A:HIS99 4.1 16.4 1.0 CG A:HIS134 4.1 18.1 1.0 ND1 A:HIS134 4.1 19.2 1.0 CG A:HIS99 4.2 15.2 1.0 CG A:ASN97 4.3 20.2 1.0 OD1 A:ASN97 4.6 19.9 1.0 O A:HOH773 4.7 27.0 0.6 O A:HOH877 4.7 35.5 1.0

J.Dong, D.Sasaki, R.Eady, S.V.Antonyuk, S.S.Hasnain. Activation of Redox Tyrosine Switch Is Required For Ligand Binding at the Catalytic Site in Heme-Cu Nitrite Reductases To Be Published.